Too much complexity! I like the simplicity of Ricky’s Weather Forecasting Stone

Too much complexity in the last few posts and related comments: multivariate analyses, path coefficients, nonparametric statistics, competing and interaction effects, explained variance, plant protein and colorectal cancer, the China Study, raw plant foods possibly giving people cancer unless they don’t …

I like simplicity though, and so does my mentor. I really like the simplicity of Ricky’s Weather Forecasting Stone. (See photo below, from … I will tell you in the comments section. Click on it to enlarge. Use the "CRTL" and "+" keys to zoom in, and CRTL" and "-" to zoom out.)

Can you guess who the gentleman on the photo is?

A few hints. He is a widely read and very smart blogger. He likes to eat a lot of saturated fat, and yet is very lean. If you do not read his blog, you should. Reading his blog is like heavy resistance exercise, for the brain. It is not much unlike doing an IQ test with advanced biology and physiology material mixed in, and a lot of joking around.

Like heavy resistance exercise, reading his blog is hard, but you fell pretty good after doing it.

Parkour Visions Summit and Talk

On August 13-15th, my friends Rafe Kelley and Tyson Cecka are hosting a parkour summit at their Seattle gym Parkour Visions. For those of you not familiar with the sport, here's a description from the Parkour Visions site:

"The essence of Parkour can be stated simply: it is the art of overcoming obstacles as swiftly and efficiently as possible using only your body. The fundamentals include running, jumping, and climbing, and we build on these fundamentals to improve our ability to pass over, under, around and through obstacles with more complex movements. Parkour is a system of fitness training that improves strength, speed, agility, co-ordination, stamina, endurance, and precision. It offers a full-body workout at any level of experience, and improves your ability to move, to harness your confidence, to change how you see the world. Parkour practitioners are called traceurs."

The summit will include seminars on strength training, injury prevention and rehab, and nutrition, as well as parkour jams, a roundtable and a dinner. I'll be giving a talk titled "Natural Eating for Sustainable Athletic Performance" on Saturday, August 14 from noon to 1:00 pm.

Registration is $40 for the whole summit. You can read a description of it here, and find a link to the registration system at the bottom of this page.

The China Study again: A multivariate analysis suggesting that schistosomiasis rules!

In the comments section of Denise Minger’s post on July 16, 2010, which discusses some of the data from the China Study (as a follow up to a previous post on the same topic), Denise herself posted the data she used in her analysis. This data is from the China Study. So I decided to take a look at that data and do a couple of multivariate analyzes with it using WarpPLS (warppls.com).

First I built a model that explores relationships with the goal of testing the assumption that the consumption of animal protein causes colorectal cancer, via an intermediate effect on total cholesterol. I built the model with various hypothesized associations to explore several relationships simultaneously, including some commonsense ones. Including commonsense relationships is usually a good idea in exploratory multivariate analyses.

The model is shown on the graph below, with the results. (Click on it to enlarge. Use the "CRTL" and "+" keys to zoom in, and CRTL" and "-" to zoom out.) The arrows explore causative associations between variables. The variables are shown within ovals. The meaning of each variable is the following: aprotein = animal protein consumption; pprotein = plant protein consumption; cholest = total cholesterol; crcancer = colorectal cancer.

The path coefficients (indicated as beta coefficients) reflect the strength of the relationships; they are a bit like standard univariate (or Pearson) correlation coefficients, except that they take into consideration multivariate relationships (they control for competing effects on each variable). A negative beta means that the relationship is negative; i.e., an increase in a variable is associated with a decrease in the variable that it points to.

The P values indicate the statistical significance of the relationship; a P lower than 0.05 means a significant relationship (95 percent or higher likelihood that the relationship is real). The R-squared values reflect the percentage of explained variance for certain variables; the higher they are, the better the model fit with the data. Ignore the “(R)1i” below the variable names; it simply means that each of the variables is measured through a single indicator (or a single measure; that is, the variables are not latent variables).

I should note that the P values have been calculated using a nonparametric technique, a form of resampling called jackknifing, which does not require the assumption that the data is normally distributed to be met. This is good, because I checked the data, and it does not look like it is normally distributed. So what does the model above tell us? It tells us that:

- As animal protein consumption increases, colorectal cancer decreases, but not in a statistically significant way (beta=-0.13; P=0.11).

- As animal protein consumption increases, plant protein consumption decreases significantly (beta=-0.19; P<0.01). This is to be expected.

- As plant protein consumption increases, colorectal cancer increases significantly (beta=0.30; P=0.03). This is statistically significant because the P is lower than 0.05.

- As animal protein consumption increases, total cholesterol increases significantly (beta=0.20; P<0.01). No surprise here. And, by the way, the total cholesterol levels in this study are quite low; an overall increase in them would probably be healthy.

- As plant protein consumption increases, total cholesterol decreases significantly (beta=-0.23; P=0.02). No surprise here either, because plant protein consumption is negatively associated with animal protein consumption; and the latter tends to increase total cholesterol.

- As total cholesterol increases, colorectal cancer increases significantly (beta=0.45; P<0.01). Big surprise here!

Why the big surprise with the apparently strong relationship between total cholesterol and colorectal cancer? The reason is that it does not make sense, because animal protein consumption seems to increase total cholesterol (which we know it usually does), and yet animal protein consumption seems to decrease colorectal cancer.

When something like this happens in a multivariate analysis, it usually is due to the model not incorporating a variable that has important relationships with the other variables. In other words, the model is incomplete, hence the nonsensical results. As I said before in a previous post, relationships among variables that are implied by coefficients of association must also make sense.

Now, Denise pointed out that the missing variable here possibly is schistosomiasis infection. The dataset that she provided included that variable, even though there were some missing values (about 28 percent of the data for that variable was missing), so I added it to the model in a way that seems to make sense. The new model is shown on the graph below. In the model, schisto = schistosomiasis infection.

So what does this new, and more complete, model tell us? It tells us some of the things that the previous model told us, but a few new things, which make a lot more sense. Note that this model fits the data much better than the previous one, particularly regarding the overall effect on colorectal cancer, which is indicated by the high R-squared value for that variable (R-squared=0.73). Most notably, this new model tells us that:

- As schistosomiasis infection increases, colorectal cancer increases significantly (beta=0.83; P<0.01). This is a MUCH STRONGER relationship than the previous one between total cholesterol and colorectal cancer; even though some data on schistosomiasis infection for a few counties is missing (the relationship might have been even stronger with a complete dataset). And this strong relationship makes sense, because schistosomiasis infection is indeed associated with increased cancer rates. More information on schistosomiasis infections can be found here.

- Schistosomiasis infection has no significant relationship with these variables: animal protein consumption, plant protein consumption, or total cholesterol. This makes sense, as the infection is caused by a worm that is not normally present in plant or animal food, and the infection itself is not specifically associated with abnormalities that would lead one to expect major increases in total cholesterol.

- Animal protein consumption has no significant relationship with colorectal cancer. The beta here is very low, and negative (beta=-0.03).

- Plant protein consumption has no significant relationship with colorectal cancer. The beta for this association is positive and nontrivial (beta=0.15), but the P value is too high (P=0.20) for us to discard chance within the context of this dataset. A more targeted dataset, with data on specific plant foods (e.g., wheat-based foods), could yield different results – maybe more significant associations, maybe less significant.

Below is the plot showing the relationship between schistosomiasis infection and colorectal cancer. The values are standardized, which means that the zero on the horizontal axis is the mean of the schistosomiasis infection numbers in the dataset. The shape of the plot is the same as the one with the unstandardized data. As you can see, the data points are very close to a line, which suggests a very strong linear association.

So, in summary, this multivariate analysis vindicates pretty much everything that Denise said in her July 16, 2010 post. It even supports Denise’s warning about jumping to conclusions too early regarding the possible relationship between wheat consumption and colorectal cancer (previously highlighted by a univariate analysis). Not that those conclusions are wrong; they may well be correct.

This multivariate analysis also supports Dr. Campbell’s assertion about the quality of the China Study data. The data that I analyzed was already grouped by county, so the sample size (65 cases) was not so high as to cast doubt on P values. (Having said that, small samples create problems of their own, such as low statistical power and an increase in the likelihood of error-induced bias.) The results summarized in this post also make sense in light of past empirical research.

It is very good data; data that needs to be properly analyzed!

Real Food XI: Sourdough Buckwheat Crepes

Buckwheat was domesticated in Southeast Asia roughly 6,000 years ago. Due to its unusual tolerance of cool growing conditions, poor soils and high altitudes, it spread throughout the Northern latitudes of Eurasia, becoming the staple crop in many regions. It's used to a lesser extent in countries closer to the equator. It was also a staple in the Northeastern US until it was supplanted by wheat and corn.

Buckwheat isn't a grain: it's a 'pseudograin' that comes from a broad-leaved plant. As such, it's not related to wheat and contains no allergenic gluten. Like quinoa, it has some unusual properties that make it a particularly nutritious food. It's about 16 percent protein by calories, ranking it among the highest protein grains. However, it has an advantage over grains: it contains complete protein, meaning it has a balance of essential amino acids similar to animal foods. Buckwheat is also an exceptional source of magnesium and copper, two important nutrients that may influence the risk of insulin resistance and cardiovascular disease (1, 2).

However, like all seeds (including grains and nuts), buckwheat is rich in phytic acid. Phyic acid complexes with certain minerals, preventing their absorption by the human digestive tract. This is one of the reasons why traditional cultures prepare their grains carefully (3). During soaking, and particularly fermentation of raw batters, an enzyme called phytase goes to work breaking down the phytic acid. Not all seeds are endowed with enough phytase to break down phytic acid in a short period of time. Buckwheat contains a lot of phytase, and consequently fermented buckwheat batters contain very little phytic acid (4, 5). It's also high in astringent tannins, but thorough soaking in a large volume of water removes them.

Buckwheat is fermented in a number of traditional cultures. In Bhutan, it's fermented to make flatbreads and alcoholic drinks (6). In Brittany (Bretagne; Northwestern France), sourdough buckwheat flour pancakes are traditional. Originally a poverty food, it is now considered a delicacy.

The following simple recipe is based on my own experimentation with buckwheat. It isn't traditional as far as I know, however it is based on traditional methods used to produce sourdough flatbreads in a number of cultures. I used the word 'crepe' to describe it, but I typically make something more akin to a savory pancake or uttapam. You can use it to make crepes if you wish, but this recipe is not for traditional French buckwheat crepes.

It's important that the buckwheat be raw and whole for this recipe. Raw buckwheat is light green to light brown (as in the photo above). Kasha is toasted buckwheat, and will not substitute properly. It's also important that the water be dechlorinated and the salt non-iodized, as both will interfere with fermentation.

For a fermentation starter, you can use leftover batter from a previous batch (although it doesn't keep very long), or rice soaking water from this method (7).

Ingredients and Materials

• 2-3 cups raw buckwheat groats
• Dechlorinated water (filtered, boiled, or rested uncovered overnight)
• Non-iodized salt (sea salt, pickling salt or kosher salt), 2/3 tsp per cup of buckwheat
  
• Fermentation starter (optional), 2 tablespoons
  
• Food processor or blender

Recipe

1. Cover buckwheat with a large amount of dechlorinated water and soak for 9-24 hours. Raw buckwheat is astringent due to water-soluble tannins. Soaking in a large volume of water and giving it a stir from time to time will minimize this. The soaking water will also get slimy. This is normal.
   
2. Pour off the soaking water and rinse the buckwheat thoroughly to get rid of the slime and residual tannins.
3. Blend the buckwheat, salt, dechlorinated water and fermentation starter in a food processor or blender. Add enough water so that it reaches the consistency of pancake batter. The smoother you get the batter, the better the final product will be.
4. Ferment for about 12 hours, a bit longer or shorter depending on the temperature and whether or not you used a starter. The batter may rise a little bit as the microorganisms get to work. The smell will mellow out. Refrigerate it after fermentation.
   
5. In a greased or non-stick skillet, cook the batter at whatever thickness and temperature you prefer. I like to cook a thick 'pancake' with the lid on, at very low heat, so that it steams gently.
   

Dig in! Its mild flavor goes with almost anything. Batter will keep for about four days in the fridge.

Thanks to Christaface for the CC licensed photo (Flickr).

My transformation: I cannot remember the last time I had a fever

The two photos below (click to enlarge) were taken 4 years apart. The one on the left was taken in 2006, when I weighed 210 lbs (95 kg). Since my height is 5 ft 8 in, at that weight I was an obese person, with over 30 percent body fat. The one on the right was taken in 2010, at a weight of 150 lbs (68 kg) and about 13 percent body fat. I think I am a bit closer to the camera on the right, so the photos are not exactly on the same scale. For a more recent transformation update, see this post.

My lipids improved from borderline bad to fairly good numbers, as one would expect, but the two main changes that I noticed were in terms of illnesses and energy levels. I have not had a fever in a long time. I simply cannot remember when it was the last time that I had to stay in bed because of an illness. I only remember that I was fat then. Also, I used to feel a lot more tired when I was fat. Now I seem to have a lot of energy, almost all the time.

In my estimation, I was obese or overweight for about 10 years, and was rather careless about it. A lot of that time I weighed in the 190s; with a peak weight of 210 lbs. Given that, I consider myself lucky not to have had major health problems by now, like diabetes or cancer. A friend of mine who is a doctor told me that I probably had some protection due to the fact that, when I was fat, I was fat everywhere. My legs, for example, were fat. So were my arms and face. In other words, I lot of the fat was subcutaneous, and reasonably distributed. In fact, most people do not believe me when I say that I weighed 210 lbs when that photo was taken in 2006; but maybe they are just trying to be nice.

If you are not obese, you should do everything you can to avoid reaching that point. Among other things, your chances of having cancer will skyrocket.

So, I lost a whopping 60 lbs (27 kg) over about 2-3 years. That is not so radical; about 1.6-2.5 lbs per month. There were plateaus with no weight loss, and even a few periods with weight gain. Perhaps because of that and the slow weight loss, I had none of the problems usually associated with body responses to severe calorie restriction, such as hypothyroidism. I remember a short period when I felt a little weak and miserable; I was doing exercise after long fasts (20 h or so), and not eating enough afterwards. I did that for a couple of weeks and decided against the idea.

There are no shortcuts with body fat loss, it seems. Push it too hard and the body will react; compensatory adaptation at work.

My weight has been stable, at around 150 lbs, for a little less than 2 years now.

What did I do to lose 60 lbs? I did a number of things at different points in time. I measured various variables (e.g., intake of macronutrients, weight, body fat, HDL cholesterol etc.) and calculated associations, using a prototype version of HealthCorrelator for Excel (HCE). Based on all that, I am pretty much convinced that the main factors were the following:

- Complete removal of foods rich in refined carbohydrates and sugars from my diet, plus almost complete removal of plant foods that I cannot eat raw. (I do cook some plant foods, but avoid the ones I cannot eat raw; with a few exceptions like sweet potato.) That excluded most seeds and grains from my diet, since they can only be eaten after cooking.

- Complete removal of vegetable oils rich in omega-6 fats from my diet. I cook primarily with butter and organic coconut oil. I occasionally use olive oil, often with water, for steam cooking.

- Consumption of plenty of animal products, with emphasis on eating the animal whole. All cooked. This includes small fish (sardines and smelts) eaten whole about twice a week, and offal (usually beef liver) about once or twice a week. I also eat eggs, about 3-5 per day.

- Practice of moderate exercise (2-3 sessions a week) with a focus on resistance training and high-intensity interval training (e.g., sprints). Also becoming more active, which does not necessarily mean exercising but  doing things that involve physical motion of some kind (e.g., walking, climbing stairs, moving things around), to the tune of 1 hour or more every day.

- Adoption of more natural eating patterns; by eating more when I am hungry, usually on days I exercise, and less (including fasting) when I am not hungry. I estimate that this leads to a caloric surplus on days that I exercise, and a caloric deficit on days that I do not (without actually controlling caloric intake).

- A few minutes (15-20 min) of direct skin exposure to sunlight almost every day, when the sun is high, to get enough of the all-important vitamin D. This is pre-sunburn exposure, usually in my backyard. When traveling I try to find a place where people jog, and walk shirtless for 15-20 min.

- Stress management, including some meditation and power napping.

- Face-to-face social interaction, in addition to online interaction. Humans are social animals, and face-to-face social interaction contributes to promoting the right hormonal balance.

When I was fat, my appetite was a bit off. I was hungry at the wrong times, it seemed. Then slowly, after a few months eating essentially whole foods, my hunger seemed to start “acting normally”. That is, my hunger slowly fell into a pattern of increasing after physical exertion, and decreasing with rest. Protein and fat are satiating, but so seem to be fruits and vegetables. Never satiating for me were foods rich in refined carbohydrates and sugars – white bread, bagels, doughnuts, pasta etc.

Looking back, it almost seems too easy. Whole foods taste very good, especially if you are hungry.

But I will never want to each a peach after I have a doughnut. The peach will be tasteless!

Minger Responds to Campbell

Hot off the presses: Dr. Colin Campbell's response to Denise Minger's China Study posts, and Minger's retort:

A Challenge and Response to the China Study

The China Study: My Response to Campbell

This is required reading for anyone who wants to evaluate Dr. Campbell's claims about the China Study data. Denise points out that Dr. Campbell's claims rest mostly on uncorrected associations, which is exactly what he was accusing Minger, Chris Masterjohn and Anthony Colpo of doing. He also appears to have selectively reported data that support his philosophy, and ignored data that didn't, even when the latter were stronger. This is true both in Dr. Campbell's book, and in his peer-reviewed papers. This type of thing is actually pretty common in the diet-health literature.

I respect everyone's food choices, whether they're omnivores, carnivores, or raw vegans, as long as they're doing it in a way that's thoughtful toward other people, animals and the environment. I'm sure there are plenty of vegans out there who are doing it gracefully, not spamming non-vegan blogs with arrogant comments.

As human beings, we're blessed and cursed with an ego, which is basically a self-esteem and self-image reinforcement machine. Since being wrong hurts our self-esteem and self-image, the ego makes us think we're right about more than we actually are. That can take the form of elaborate justifications, and the more intelligent the person, the more elaborate the justifications. An economic policy that makes you richer becomes the best way to improve everyone's bottom line. A dietary philosophy that was embraced for humane reasons becomes the path to optimum health... such is the human mind. Science is basically an attempt to remove as much of this psychic distortion as possible from an investigation. Ultimately, the scientific method requires rigorous and vigilant stewardship to achieve what it was designed to do.

Subcutaneous versus visceral fat: How to tell the difference?

The photos below, from Wikipedia, show two patterns of abdominal fat deposition. The one on the left is predominantly of subcutaneous abdominal fat deposition. The one on the right is an example of visceral abdominal fat deposition, around internal organs, together with a significant amount of subcutaneous fat deposition as well.

Body fat is not an inert mass used only to store energy. Body fat can be seen as a “distributed organ”, as it secretes a number of hormones into the bloodstream. For example, it secretes leptin, which regulates hunger. It secretes adiponectin, which has many health-promoting properties. It also secretes tumor necrosis factor-alpha (more recently referred to as simply “tumor necrosis factor” in the medical literature), which promotes inflammation. Inflammation is necessary to repair damaged tissue and deal with pathogens, but too much of it does more harm than good.

How does one differentiate subcutaneous from visceral abdominal fat?

Subcutaneous abdominal fat shifts position more easily as one’s body moves. When one is standing, subcutaneous fat often tends to fold around the navel, creating a “mouth” shape. Subcutaneous fat is easier to hold in one’s hand, as shown on the left photo above. Because subcutaneous fat tends to “shift” more easily as one changes the position of the body, if you measure your waist circumference lying down and standing up, and the difference is large (a one-inch difference can be considered large), you probably have a significant amount of subcutaneous fat.

Waist circumference is a variable that reflects individual changes in body fat percentage fairly well. This is especially true as one becomes lean (e.g., around 14-17 percent or less of body fat for men, and 21-24 for women), because as that happens abdominal fat contributes to an increasingly higher proportion of total body fat. For people who are lean, a 1-inch reduction in waist circumference will frequently translate into a 2-3 percent reduction in body fat percentage. Having said that, waist circumference comparisons between individuals are often misleading. Waist-to-fat ratios tend to vary a lot among different individuals (like almost any trait). This means that someone with a 34-inch waist (measured at the navel) may have a lower body fat percentage than someone with a 33-inch waist.

Subcutaneous abdominal fat is hard to mobilize; that is, it is hard to burn through diet and exercise. This is why it is often called the “stubborn” abdominal fat. One reason for the difficulty in mobilizing subcutaneous abdominal fat is that the network of blood vessels is not as dense in the area where this type of fat occurs, as it is with visceral fat. Another reason, which is related to degree of vascularization, is that subcutaneous fat is farther away from the portal vein than visceral fat. As such, it has to travel a longer distance to reach the main “highway” that will take it to other tissues (e.g., muscle) for use as energy.

In terms of health, excess subcutaneous fat is not nearly as detrimental as excess visceral fat. Excess visceral fat typically happens together with excess subcutaneous fat; but not necessarily the other way around. For instance, sumo wrestlers frequently have excess subcutaneous fat, but little or no visceral fat. The more health-detrimental effect of excess visceral fat is probably related to its proximity to the portal vein, which amplifies the negative health effects of excessive pro-inflammatory hormone secretion. Those hormones reach a major transport “highway” rather quickly.

Even though excess subcutaneous body fat is more benign than excess visceral fat, excess body fat of any kind is unlikely to be health-promoting. From an evolutionary perspective, excess body fat impaired agile movement and decreased circulating adiponectin levels; the latter leading to a host of negative health effects. In modern humans, negative health effects may be much less pronounced with subcutaneous than visceral fat, but they will still occur.

Based on studies of isolated hunger-gatherers, it is reasonable to estimate “natural” body fat levels among our Stone Age ancestors, and thus optimal body fat levels in modern humans, to be around 6-13 percent in men and 14–20 percent in women.

If you think that being overweight probably protected some of our Stone Age ancestors during times of famine, here is one interesting factoid to consider. It will take over a month for a man weighing 150 lbs and with 10 percent body fat to die from starvation, and death will not be typically caused by too little body fat being left for use as a source of energy. In starvation, normally death will be caused by heart failure, as the body slowly breaks down muscle tissue (including heart muscle) to maintain blood glucose levels.

References:

Arner, P. (2005). Site differences in human subcutaneous adipose tissue metabolism in obesity. Aesthetic Plastic Surgery, 8(1), 13-17.

Brooks, G.A., Fahey, T.D., & Baldwin, K.M. (2005). Exercise physiology: Human bioenergetics and its applications. Boston, MA: McGraw-Hill.

Fleck, S.J., & Kraemer, W.J. (2004). Designing resistance training programs. Champaign, IL: Human Kinetics.

Taubes, G. (2007). Good calories, bad calories: Challenging the conventional wisdom on diet, weight control, and disease. New York, NY: Alfred A. Knopf.